Run ID: ERR4798686
Sample name:
Date: 20-10-2023 03:05:02
Number of reads: 3723128
Percentage reads mapped: 99.7
Strain: lineage3.1.2.1
Drug-resistance: XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.His445Asp (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Met306Ile (0.99) |
| Pyrazinamide | R | pncA c.419_420dupGC (0.95) |
| Streptomycin | R | rpsL p.Lys43Arg (0.99) |
| Fluoroquinolones | R | gyrA p.Asp94Asn (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Asn (1.00) |
| Ofloxacin | R | gyrA p.Asp94Asn (1.00) |
| Levofloxacin | R | gyrA p.Asp94Asn (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Asn (1.00) |
| Aminoglycosides | R | rrs n.1401A>G (1.00) |
| Amikacin | R | rrs n.1401A>G (1.00) |
| Capreomycin | R | rrs n.1401A>G (1.00) |
| Kanamycin | R | rrs n.1401A>G (1.00) |
| Cycloserine | ||
| Ethionamide | R | ethA c.858_859insG (1.00), ethA c.858_859insG (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid | R | rplC p.Cys154Arg (0.99) |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage3 | East-African-Indian | CAS | RD750 | 1.0 |
| lineage3.1 | East-African-Indian | Non-CAS1-Delhi | RD750 | 1.0 |
| lineage3.1.2 | East-African-Indian | CAS;CAS2 | RD750 | 1.0 |
| lineage3.1.2.1 | East-African-Indian | CAS2 | RD750 | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7581 | p.Asp94Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 0.99 | streptomycin |
| rplC | 801268 | p.Cys154Arg | missense_variant | 0.99 | linezolid |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2288821 | c.419_420dupGC | frameshift_variant | 0.95 | pyrazinamide |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
| ethA | 4326615 | c.858_859insG | frameshift_variant | 1.0 | ethionamide, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 |
| rpoC | 762434 | c.-936T>G | upstream_gene_variant | 0.99 |
| rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
| rpoC | 764501 | p.Val378Leu | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102094 | p.Val317Met | missense_variant | 0.99 |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
| PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.98 |
| PPE35 | 2169938 | c.675C>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 |
| eis | 2715393 | c.-61A>G | upstream_gene_variant | 1.0 |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 |
| ribD | 2986827 | c.-12G>A | upstream_gene_variant | 1.0 |
| thyA | 3074648 | c.-177T>C | upstream_gene_variant | 0.97 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| embC | 4242075 | p.Arg738Gln | missense_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338346 | p.Arg59Gln | missense_variant | 0.96 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
| Rv1258c | 1406835 | c.384_505del | frameshift_variant | 0.98 |
